Here's a similar question on preventing flickering with Bootstrap-Select.
The fact is that a Flash of Unstyled Content (FOUC) is going to happen anytime that JavaScript is running on the client after the page has rendered and changes the appearance of the page. You're best bet is to just minimize the changes ahead of time.
The heavy handed approach would be to wait to display the page until all the scripts have run, but this is much worse for users.
As Roryok suggested, the best way to mitigate this issue is to style the appearance of the native element as close as possible to the plugin control.
To do that, just add the following css to any select element which will be applied before the javascript renders the control.
/* apply styles to original select element before hidden */
select.select2{
color: #444;
background-color: #FFF;
border: 1px solid #AAA;
border-radius: 4px;
box-sizing: border-box;
cursor: pointer;
display: block;
height: 28px;
padding-left: 5px;
font: unset;
}
Demo in Stack Snippets
<!-- begin snippet: js hide: false console: false babel: false -->
<!-- language: lang-js -->
$('.select2').select2();
<!-- language: lang-css -->
body {
display: flex;
flex-direction: row;
}
div {
padding: 15px;
display: flex;
flex-direction: column;
}
label {
font-weight: bold;
}
select {
min-width: 150px;
}
.select2-theme {
color: #444;
background-color: #FFF;
border: 1px solid #AAA;
border-radius: 4px;
box-sizing: border-box;
cursor: pointer;
display: block;
height: 28px;
padding-left: 5px;
font: unset;
}
<!-- language: lang-html -->
<link href="https://cdnjs.cloudflare.com/ajax/libs/select2/4.0.7/css/select2.css" rel="stylesheet" />
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/2.2.4/jquery.js"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/select2/4.0.7/js/select2.js"></script>
<div >
<label>Select 2</label>
<select class="select2">
<option>Mustard</option>
<option>Ketchup</option>
<option>Relish</option>
</select>
</div>
<div>
<label>Select2 Themed</label>
<select class="select2-theme">
<option>Mustard</option>
<option>Ketchup</option>
<option>Relish</option>
</select>
</div>
<div>
<label>Default Select</label>
<select >
<option>Mustard</option>
<option>Ketchup</option>
<option>Relish</option>
</select>
</div>
<!-- end snippet -->